As far as I can tell. The 68060.library version 2.2 which is from the Blizzard floppy is still there. With my A4000 if those are missing, it won't boot at all especially the 040 dummy lib. Maybe I should double check with that floppy. I was trying to see if I had a newer version of the 060 library. I will dig out my Blizzard docs too.
It acts like an 060. When it boots, I get that cycle of rainbow colors and it reboots again and comes to Workbench. Showconfig shows I have an 060 processor. It acts like the exec.lib maybe wrong because I believe that handles all the system stuff that errors?
I figured this should be a slam dunk. Just use the option of upgrading 3.5 to 3.9. When I try to apply BB1, it gets stuck at 40% updating. I see no disk activity. I left it for over an hour. After I installed 3.9 natively, BB1 the "Installer" throws that 80000004 error.